Learning the CONN Toolbox for Functional Connectivity Analysis


Fall 2021 dates:
5 Mondays – Nov 22, 29, Dec 6, 13, 20

Resting-state functional connectivity has taken the brain imaging community by storm. Five to ten minutes of MRI data collection from almost any subject or patient can reveal organized systems of activity in the brain that can be used in a wide variety of ways for basic and clinical research, and even to guide non-invasive brain stimulation. The primary tool for analyzing such data has been correlation-based analysis of the connections between seed regions in the brain. A premier software package for such analysis is the CONN toolbox, created by Susan Whitfield-Gabrieli and Alfonso Nieto Castañòn.

CONN is an SPM-based toolbox for functional connectivity analyses in the resting state and during tasks. It is ranked as one of the top 10 most visited and downloaded neuroimaging tools and resources at NITRC, with over 40,000 downloads and a very active user community. Also, it has been cited and used in over 400 papers (the second-most cited reference in the Brain Connectivity journal).

The program consists of three intensive days of training in the use of this software. Participants will bring their own laptop computers; classroom presentations will be followed by substantial time using the packages with expert guidance available.

Software description

CONN is an open-source Matlab/SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs. Processing and analysis steps in CONN include:

  • Importing DICOM, ANALYZE, and NIfTI functional and anatomical files, either raw or partially/fully preprocessed volumes. Automatic import tools forBIDSdatasets and fMRIPrep outputs
  • Standardized preprocessing pipelines of functional and anatomical volumes powered by SPM12 (including susceptibility distortion correction, motion correction / realignment, slice-timing correction, outlier identification, coregistration, tissue-class segmentation, MNI-normalization, and smoothing)
  • Control of residual physiological and motion artifacts (e.g. scrubbing, aCompCor, ICA-based denoising, Global Regression, band-pass filtering)
  • Integrated quality control procedures and measures (e.g. FC histogram plots, BOLD signal carpetplots, Framewise Displacement, GCOR measures, FC-QC correlations)
  • Multipleconnectivity analyses and measures, including Seed-Based Correlations (SBC), ROI-to-ROI analyses, complex-network analyses, generalized Psycho-Physiological Interaction models (gPPI), Independent Component Analyses (group-ICA), masked ICA, Amplitude of Low-Frequency Fluctuations (ALFF & fALFF), Intrinsic Connectivity (ICC), Local Homogeneity (LCOR), Global Correlations (GCOR), Multivoxel Pattern Analyses (MVPA), and dynamic connectivity analyses (dyn-ICA, sliding-window correlations)
  • Group- and population-level inferencesand models, including ANOVA, regression, longitudinal, experimental, and mixed within- and between-subject designs. Univariate and Multivariate statistics. Control for multiple comparisons using parametric (e.g. Random Field Theory), and non-parametric permutation/randomization techniques (e.g. Threshold Free Cluster Enhancement)




The faculty for the program includes the originators and developers of the CONN Toolbox and several expert users and teachers to help with the interactive portion of the training:

Susan Whitfield-Gabrieli: Software developer and principal speaker at this program. She was a keynote speaker at the 2015 meeting of the Organization for Human Brain Mapping, speaking on the topic of Connectomic Insights into Psychiatric Disorders.
Alfonso Nieto Castañòn: A prize-winning Matlab Programmer; software developer of CONN; an active computational neuroscientist researcher.
Sheeba Arnold Anteraper: Senior Programmer at the McGovern Institute, and an expert user of CONN.
Robert L. Savoy: Organizer of numerous brief, intense training programs at the Martinos Center for Biomedical Imaging of the Massachusetts General Hospital and elsewhere around the world.



Please include an informal statement describing your background (academic, clinical, research, industrial, other), your experience with functional neuroimaging, fMRI, and resting state connectivity analysis. This is also an opportunity to state what you most hope to get out of the program. This biosketch will be distributed to the faculty and to other course participants. It should be no more than two paragraphs in length. PLEASE: Make the biosketch informal. It is intended to introduce you to the other participants and staff, not to apply for a job.
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If you are paying by fund number, we will contact you for further information.
The fee for the program is $1500. A reduced rate of $1000 is available to graduate students with a letter of verification from their Department Chairman. NOTE: MD's and Phd's do not qualify for the graduate student rate and normally are expected to pay the full fee. However, if a post-doctoral applicant is paying out-of-pocket (rather than the more normal grant-funded or institutionally-funded payment) then a discounted rate of $1250 is available. Please contact us should special arrangements need to be made regarding payment. Course fees are refundable up to 30 days prior to the session. A $200 fee will be deducted, should you cancel and request a refund between 30 days and 21 days (3 weeks) prior to the program start. After that, the tuition can be applied to a future program, or can be 50% refunded. Please email fmrivfp@mgh.harvard.edu with any questions.


Sample Schedule

The details and exact order of the schedule below are likely to be modified as the program approaches.   Information from registrants about adding specific topics will be strongly considered and accommodated if possible.

 The “Final Application Lecture” may be re-scheduled to a time earlier in the week; perhaps the end of one of the days (probably Wednesday), or after a group dinner on that evening.



Morning Program Introduction Susan Whitfield-Gabrieli
Approaches to MultiVariate Analysis and Functional Connectivity Robert Savoy
MATLAB and its Relationship to The CONN Toolbox faculty
Orientation to Relevant Software Packages Susan Whitfield-Gabrieli
 Afternoon Resting State Connectivity: History; Examples; Cautionary Stories Susan Whitfield-Gabrieli
Orientation to the Specifics of the CONN Toolbox     faculty
Preprocessing: Artifact Prevention, Detection, and Mitigation Susan Whitfield-Gabrieli
Homework Assignment: Preprocessing


Morning Homework Review: Preprocessing
Single Subject Processing in CONN Susan Whitfield-Gabrieli
Homework Assignment: Single Subject Processing
Afternoon Single Group Second-Level Design Susan Whitfield-Gabrieli
Single Group Second-Level Estimation Susan Whitfield-Gabrieli
Homework Assignment: Single Group


Morning Homework Review: First Level Analysis
Multiple Group Second-Level Design Alfonso Nieto Castañón
Multiple Group Second-Level Estimation Alfonso Nieto Castañón
Homework: Second Level (NYU Group Data)
Afternoon Review/Discussion of Basic CONN Toolbox faculty
Overview of Advanced Features in the CONN Toolbox: Alfonso Nieto Castañón
     ROI-to-ROI Analyses
     Graph Theory
     Voxel-to-Voxel Analyses
     Surface-Based Analysis
     Dynamic Connectivity
     Latest CONN Features:


Morning Homework Review: Second Level Analysis
Connectome Analysis: ROI-to-ROI Alfonso Nieto Castañón
Connectome Analysis: Graph Theory Alfonso Nieto Castañón
Homework: ROI-to-ROI & Graph Theory
Afternoon Connectome Analysis: Voxel-to-Voxel Alfonso Nieto Castañón
Connectome Analysis: Surface-Based Alfonso Nieto Castañón
Homework: Voxel-to-Voxel & Surface-Based


Morning Homework Review: Voxel-to-Voxel & Surface
Connectome Analysis: PPI Alfonso Nieto Castañón
Connectome Analysis: Dynamic Connectivity Alfonso Nieto Castañón
Connectome Analysis: Latest Features Alfonso Nieto Castañón
Homework-during-Lunch! PPI & Dynamic Connectivity
Afternoon Homework Review: PPI & Dynamic Connectivity
Final Application Lecture (may be scheduled earlier in week) Susan Whitfield-Gabrieli
Informal Discussion faculty